I have a question related to the transition settings. I have a peptide, 9 residues, in which I would like to see the M+4 precursor. This does not appear from the list when I expand the precursor list of this peptide, but it does for longer peptides. Is there a way to select, also for shorter peptides, the precursor M+4? It would be interesting because I need to check the incorporation of 13C into it and therefore I need this information.
Nick Shulman responded:
At "Settings > Transition Settings > Full Scan" you have a little bit of control over how many isotope peaks you get using the "Isotope Peaks Included" setting.
However, regardless of that setting, Skyline will never let you add a mass whose predicted abundance is less than 1% of most abundant isotope. So, for smaller peptides you really may be limited to only two or three isotope masses.